I can only guess as what might be doing it. It could be the "Trust junk mail headers in messages." It may color it brown, but since its filter didn't identify it as junk, it didn't mark it as such.
I don't have any to check, so you'll have to look at the long headers of those emails and see if they have a spam header.
Just checked my rules. The only one is the Default Apple Mail and that's blue.
I can confirm that there has been a new update to Mail within the last week. This caught many people on the hop because it was not compatible with OS X 10.8.3 and they had to upgrade to 10.8.5.
Looking even deeper, it's not compatible with 10.8.5 either.
Well, some versions....
The message they get is:-
You cannot use this version of Mail with this version of Mac OS X.
You have Mail version 6.6(1510/1508). It cannot be used on Mac OS X Version 10.8.5 (build 12F37). For more information click the help button.
Guess what I have?
Mail 6.6 (1510)
OS X 10.8.5 (12F37)
As I said in my original post, I suspected some silent updates because of a few oddities that suddenly occurred. Prior to finding these, I had noticed some unusual flashing lights on my broadband box while I was watching TV - not using my computer. Actually, I got up and pulled the plug - fearing Wifi-jackers. I have since changed my update settings to download but don't install. I didn't get the message - possibly because of the silent install, or pulling the plug.
There are two options. one is:-
".... downloading and installing the 10.8.5 Combo Update on top of the 10.8.5 update pushed from Software Update (App Store) solves the issue."
The other involves booting from the repair disk and choosing "Re-install OS X".
I think I'll try the Combo and see if that fixes things.
Watch this space.
Sorry for the delay. I turned my back on this question due to the constant intervention of an individual, whom I now believe, may have "intellectual issues." I am from the UK and we call a spade, a spade....
The answer is "Sort of, Maybe, NO".
I bought my "Late 2009" iMac in Spring 2010. The installation disks were for Snow Leopard. I subsequently upgraded to Lion and Mountain Lion on-line. So, by the time I had my problem, my system was a mish-mash of Snow Leopard + Updates, Lion + Updates and Mountain Lion + Updates. "A bit of a dogs dinner", as we say on this side of the pond. SHAME ON APPLE for not providing the option for new installation disks when you upgrade.
I had previously got screwed on up something, (can't remember what) and decided to re-install. So I loaded Snow Leopard from CD and upgraded to Lion via Apple Store and later upgraded to Mountain Lion. 'Can't fault Apple Store for remembering what I'd paid for. But what intermediate upgrades did I, should I, have include? I Dunno.
SO, I came to this problem after a Mountain Lion upgrade. I thought that I would reload, again, from SL etc. etc....
'Didn't work. Why? Because the Snow Leopard installation disks were not compatible with the Mountain Lion Installer. This was compounded by having Bluetooth problems which meant that the "cmd" key functions weren't being obeyed. ('Didn't help that, errm, Ham Shanks were going on about the "Option" key, when there is no "Option" key on a UK keyboard.[It's labelled "alt"])
No matter how many times I specified this, I kept being told the same failed procedures. Is there a name for people who give the same advice, thus boosting their help scores and and their egos, making it look as if they know what they are talking about, when they don't?
I shall call them Parasites.
So - What Did I Do? Google is my Friend. I found out how to create a Mountain Lion Bootable Startup Disk. You need an 8GB memory stick, or, as in my case, a Dual Layer DVD (which the iMac will write). Of course, you have to have a valid copy of Mountain Lion from the App site. Once you have paid for software, you are permitted to make a backup copy. You are not permitted to pass your copy to a third party. No, Apple do not tell you how.
I reloaded my system from my bootable DVD, applied ALL the Mountain Lion upgrades INCLUDING the Extra Final (for now) upgrade to 10.8.5 and everything seems to work.
Except for one old email, which I can't get to change it's status from Junk to Not Junk. All the new stuff works OK, though.
My advice, if not too late, is to apply all the updates, including the "Last of the Last (Maybe)". If it still doesn't work, build a bootable ML DVD.
Save what needs saving and try installing "over the top". Then go through all of the ML upgrades, including the "Last of the Last"
If that doesn't work, Install "New" (trash your disks, erase, rebuild and reinstall) then restore. Or, if you haven't got anything that you want to save, just erase and rebuild.
So, "Sort Of, Maybe, No"
Hope this sort of helps.
A set up that started at OS X 10.6(.0) and had the Updates as they occurred and then had OS X 10.7 installed and it's follow up updates in turn followed by OS X 10.8 will follow a slightly different path on a Reinstall from a clean OS X 10.6
If you then install Lion (OS X 10.7) it will download and Install the latest version of that when using the App Store.
This will be repeated for Mountain Lion.
For me I prefer my Junk Button to be on the right near my Delete Button but as a separate item.
I prefer the ability to "miss" when trying to Click it rather than sometimes deleting something.
My Mail > View Menu > Customise Tool Bar looks like this:-
I must admit I have reduced the size of this pic but I hope you can see enough detail.
With the red text I highlight the default Layout (Delete and Junk together with Junk on the right)
I use the blue option - individual icons dragged into the order I want/prefer
The green items point out an alternative Dual Button but junk on the Left.
The Blue one also highlights that if you select an item in the Junk folder the icon Changes as does it's action.
I see from earlier pics Barney seems to be using the default (red) layout.
I also have things moved to a Junk Folder
This Junk Folder is what is behind the Custom settings.
I am not sure what you meant by round and oblong buttons.
iMac 2.5Ghz 5i 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad
Your answer is basically the same as mine. Coming to 10.8 by installing 10.6, then updates, then 10.7, then updates, then 10.8, then updates, does not end up as quite the same as starting from 10.8 and installing ALL ITS updates. The only way around this is to install 10.8 from external media.
The problem is that Apple does not supply the media to upgrade directly to 10.8, unless you bought a Mac with 10.8. The solution is to create a 10.8 bootable installation device (memory stick or DVD DL) from your legitimately purchased version of 10.8 thus:-
As for the oblong buttons, they occur on the top right hand side of the yellow/brown header which is displayed when you expand a yellow/brown junk mail from the "Sort By" or middle column.
Anyway, it doesn't matter. Junk mail processing went faulty for myself and other people. After a bootable install of 10.8 and full update (OS X 10.8.5 (12F45) it seems to have sorted itself. It's history.
I had the same thing today (a non-junk messages was in my Gmail IMAP Junk folder, and there was no 'not-junk button to click).
If you simply drag the message onto your GMail inbox icon, it seems to tell Gmail (and Mac mail) it's not junk. In other words, move the message out of the junk folder into the inbox.